Man pages for IOBR/IOBR
Immune Oncology Biological Research
| add_riskscore | Add Risk Score to Dataset |
| anno_eset | Annotating gene expression matrix and remove duplicated genes |
| assimilate_data | Assimilate data with similar columns |
| batch_cor | Batch Correlation Analysis |
| batch_kruskal | batch_kruskal |
| batch_pcc | Batch way to calculate the partial correlation coefficient |
| batch_sig_surv_plot | Batch Signature Survival Plot |
| batch_surv | batch_surv - Batch Survival Analysis Function |
| batch_wilcoxon | Batch to conduct wilcoxon test between two groups |
| best_cutoff | Extract best cut-off and add new binary object to data frame |
| best_cutoff2 | Extract best cut-off and add new binary object to data frame |
| BinomialAUC | Calculate Area Under the Curve (AUC) for Binomial Model |
| BinomialModel | Binomial Model Construction |
| break_month | Break Time Into Blocks |
| CalculatePref | Calculate Performance Metrics |
| calculate_sig_score | Calculating signature score on a gene expression dataset |
| calculate_sig_score_integration | Calculating signature score using Integration method |
| calculate_sig_score_pca | Calculating signature score using PCA method |
| calculate_sig_score_ssgsea | Calculating signature score using ssGSEA method |
| calculate_sig_score_zscore | Calculating signature score using z-score method |
| CalculateTimeROC | Calculate Time-Dependent ROC |
| cell_bar_plot | Visualize the results as a stacked bar chart with... |
| check_cancer_types | Process Batch Table and Check Cancer Types |
| check_eset | check_eset - Check integrity and outliers of expression set |
| CIBERSORT | CIBERSORT is an analytical tool developed by Newman et al. to... |
| combine_pd_eset | combine pdata and eset |
| Construct_con | Construct Contrast Matrix |
| ConvertRownameToLoci | Convert Rowname To Loci |
| CoreAlg | Title CoreAlg |
| count2tpm | Convert read counts to transcripts per million (TPM) |
| creat_folder | Title creates a new folder or directory |
| deconvo_cibersort | Decoding immune microenvironment using CIBERSORT |
| deconvo_epic | Estimating immune microenvironment using EPIC: FOR RNAseq... |
| deconvo_estimate | Calculation of stromal, immune, and ESTIMATE scores |
| deconvo_ips | Calculating immune phenotype score using IPS |
| deconvolute_quantiseq.default | Use quanTIseq to deconvolute a gene expression matrix. |
| deconvolute_timer.default | Deconvolute Tumor Microenvironment Using TIMER |
| deconvo_mcpcounter | Estimating immune microenvironment using MCP-counter |
| deconvo_quantiseq | Deconvoluting micrornvironment using the quanTIseq technique |
| deconvo_ref | Estimate the fraction of cell types using defined reference... |
| deconvo_timer | Deconvoluting using the TIMER technique |
| deconvo_tme | Deconvoluting Tumor microenvironment on a transcriptomic... |
| deconvo_xcell | Decoding immune microenvironment using xCell |
| design_mytheme | design_mytheme |
| doPerm | Title |
| DrawQQPlot | Draw QQ Plot Comparing Cancer and Immune Expression |
| Enet | Elastic Net Model Fitting |
| enrichment_barplot | Enrichment bar plot with two directions |
| EPIC | Estimate the proportion of immune and cancer cells. |
| eset_distribution | Title eset_distribution |
| estimateScore | estimateScore |
| exact_pvalue | Calculate Exact P-value for Correlation |
| extract_sc_data | Extract data frame |
| feature_manipulation | feature_manipulation - Manipulate features in a matrix or... |
| feature_select | Feature Selection |
| filterCommonGenes | filterCommonGenes |
| find_markers_in_bulk | Find markers in bulk |
| find_mutations | Mutation Analysis Related to Signature Scores |
| find_outlier_samples | Identification of Potential Outlier Samples in Gene... |
| find_variable_genes | find_variable_genes |
| format_msigdb | Format input signatures from MsgiDB |
| format_signatures | Transform signature gene data into list format |
| generateRef | Generate Reference Signature Matrix |
| generateRef_DEseq2 | Generate Reference Signature Matrix using DESeq2 |
| generateRef_limma | Generate Reference Signature Matrix Using Limma |
| generateRef_rnaseq | Generate Reference Gene Matrix from DEGs Using RNA-seq Data |
| generateRef_seurat | generateRef_seurat |
| get_cols | Set and view the color palettes |
| get_cor | Calculate and Visualize Correlation between Two Variables |
| get_cor_matrix | Calculate and Visualize Correlation Matrix between Two... |
| GetFractions.Abbas | Constrained regression method implemented in Abbas et al.,... |
| getHRandCIfromCoxph | Extract hazard ratio and confidence intervals from a coxph... |
| GetOutlierGenes | Get Outlier Genes |
| get_sig_sc | get_sig_sc |
| high_var_fea | Extract most variable features form statistical results |
| iobr_cor_plot | Integrative Correlation Between Phenotype and Features |
| iobr_deconvo_pipeline | Tumor Microenvironment Analysis Pipeline |
| iobr_deg | Differential Expression Analysis |
| iobr_pca | Principal Component Analysis (PCA) Visualization |
| IPS_calculation | This R-script can be used to calculate Immunophenoscore (IPS) |
| ipsmap | calculate Immunophenoscore Title |
| lasso_select | Extract features of Predictive or Prognostic Model Using... |
| limma.dif | Differential Expression Analysis Using Limma |
| log2eset | Judge whether the expression set needs log2 transformation |
| LR_cal | LR_cal |
| make_mut_matrix | Make mutation matrix using maf data |
| mapbw | Map Black and White Colors Based on Input Value |
| mapcolors | Map Colors Based on Input Value |
| merge_duplicate | Merge Data Frames Handling Duplicated Column Names |
| merge_duplicates | Merging the duplicates from the input matrix. |
| merge_eset | Merge expression sets by row names |
| microenvironmentScores | Calculate microenvironment scores |
| mouse2human_eset | Converting mouse gene symbol to human gene symbol of... |
| outputGCT | outputGCT |
| output_sig | save signature data into a data frame |
| palettes | Choose colors. |
| ParseInputExpression | Parse Input Gene Expression Data |
| percent_bar_plot | Create a Percent Bar Plot |
| pie_chart | pie_chart |
| PlotAUC | Plot AUC ROC Curves |
| plotPurity | plotPurity |
| PlotTimeROC | Plot Time-Dependent ROC Curves |
| ProcessingData | Processing Data for Model construction |
| PrognosticAUC | Calculate Prognostic Area Under the Curve (AUC) |
| PrognosticModel | Prognostic Modeling for Survival Data |
| PrognosticResult | Prognostic Results for Survival Models |
| quantiseq_helper | Helper functions for quanTIseq |
| rawEnrichmentAnalysis | Calculated raw xCell enrichment scores |
| rbind_iobr | rbind_iobr |
| RegressionResult | Regression Result Computation |
| remove_batcheffect | Removing batch effect of two or three expression set |
| RemoveBatchEffect | Remove batch effect of expression set |
| remove_duplicate_genes | Remove Duplicate Gene Symbols in Gene Expression Data |
| remove_names | Batch to transform patterns to special character |
| roc_time | roc_time |
| scaleCounts | Scaling raw counts from each sample. |
| scale_matrix | scale_matrix - Scale and manipulate a matrix |
| select_method | Choose which method to conduct following analysis |
| sig_box | Title: sig_box - Generate a Box plot with Statistical... |
| sig_box_batch | Title sig_box_batch |
| sig_forest | Forest Plot for Survival Analysis Results |
| sig_gsea | sig_gsea - Perform Gene Set Enrichment Analysis |
| sig_heatmap | sig_heatmap |
| signature_score_calculation_methods | List of supported signature score calculation methods |
| sig_pheatmap | Title sig_pheatmap |
| sig_roc | Plot ROC Curves and Compare Them |
| sigScore | Calculate siganture score using PCA function |
| sig_surv_plot | Multiple survival KM-plot to a signature or gene |
| spillOver | Adjust scores using the spillover compensation method |
| SplitTrainTest | Split Data into Training and Testing Sets |
| subgroup_survival | Title Extract hazard ratio and confidence intervals from a... |
| surv_group | Generate Kaplan-Meier Survival Plots for Categorical Groups |
| tcga_rna_preps | Title tcga_rna_preps |
| timer_available_cancers | TIMER signatures are cancer specific. This is the list of... |
| TimerINFO | Source code for the TIMER deconvolution method. |
| tme_cluster | Identification of TME cluster |
| tme_deconvolution_methods | Collection of tumor microenvironment cell fraction... |
| Top_probe | Top Probe Selector |
| transform_data | Transform features with Inf or NA to other number |
| transformScores | Transform scores from raw scores to fractions |
| xCellAnalysis | The xCell analysis pipeline |
| xCellSignifcanceBetaDist | Calculate significance p-values for the null hypothesis that... |
| xCellSignifcanceRandomMatrix | Calculate significance p-values for the null hypothesis that... |
